adds group parameter to chimera.uchime so you can check for chimeras with template...

[mothur.git] / commandfactory.cpp

diff --git a/commandfactory.cpp b/commandfactory.cpp
index fbafe572582194ca455074a4c4fab0887a21bf0c..8e61e6e7ecef2bf38ea19ddb9171312bae3ade7b 100644 (file)
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -69,6 +69,7 @@
 #include "chimeraslayercommand.h"
 #include "chimerapintailcommand.h"
 #include "chimerabellerophoncommand.h"
+#include "chimerauchimecommand.h"
 #include "setlogfilecommand.h"
 #include "phylodiversitycommand.h"
 #include "makegroupcommand.h"
@@ -117,6 +118,10 @@
 #include "setcurrentcommand.h"
 #include "sharedcommand.h"
 #include "getcommandinfocommand.h"
+#include "deuniquetreecommand.h"
+#include "countseqscommand.h"
+#include "countgroupscommand.h"
+#include "clearmemorycommand.h"
 
 /*******************************************************/
 
@@ -184,7 +189,7 @@ CommandFactory::CommandFactory(){
        commands["trim.flows"]                  = "trim.flows";
        commands["list.seqs"]                   = "list.seqs";
        commands["get.seqs"]                    = "get.seqs";
-       commands["remove.seqs"]                 = "get.seqs";
+       commands["remove.seqs"]                 = "remove.seqs";
        commands["system"]                              = "system";
        commands["align.check"]                 = "align.check";
        commands["get.sharedseqs"]              = "get.sharedseqs";
@@ -238,6 +243,10 @@ CommandFactory::CommandFactory(){
        commands["get.current"]                 = "get.current";
        commands["set.current"]                 = "set.current";
        commands["get.commandinfo"]             = "get.commandinfo";
+       commands["deunique.tree"]               = "deunique.tree";
+       commands["count.seqs"]                  = "count.seqs";
+       commands["count.groups"]                = "count.groups";
+       commands["clear.memory"]                = "clear.memory";
        commands["pairwise.seqs"]               = "MPIEnabled";
        commands["pipeline.pds"]                = "MPIEnabled";
        commands["classify.seqs"]               = "MPIEnabled"; 
@@ -247,6 +256,7 @@ CommandFactory::CommandFactory(){
        commands["chimera.ccode"]               = "MPIEnabled";
        commands["chimera.check"]               = "MPIEnabled";
        commands["chimera.slayer"]              = "MPIEnabled";
+       commands["chimera.uchime"]              = "chimera.uchime";
        commands["chimera.pintail"]             = "MPIEnabled";
        commands["chimera.bellerophon"] = "MPIEnabled";
        commands["screen.seqs"]                 = "MPIEnabled";
@@ -351,6 +361,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "chimera.ccode")                 {       command = new ChimeraCcodeCommand(optionString);                        }
                else if(commandName == "chimera.check")                 {       command = new ChimeraCheckCommand(optionString);                        }
                else if(commandName == "chimera.slayer")                {       command = new ChimeraSlayerCommand(optionString);                       }
+               else if(commandName == "chimera.uchime")                {       command = new ChimeraUchimeCommand(optionString);                       }
                else if(commandName == "chimera.pintail")               {       command = new ChimeraPintailCommand(optionString);                      }
                else if(commandName == "chimera.bellerophon")   {       command = new ChimeraBellerophonCommand(optionString);          }
                else if(commandName == "phylotype")                             {       command = new PhylotypeCommand(optionString);                           }
@@ -406,6 +417,10 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
                else if(commandName == "anosim")                                {       command = new AnosimCommand(optionString);                                      }
                else if(commandName == "make.shared")                   {       command = new SharedCommand(optionString);                                      }
                else if(commandName == "get.commandinfo")               {       command = new GetCommandInfoCommand(optionString);                      }
+               else if(commandName == "deunique.tree")                 {       command = new DeuniqueTreeCommand(optionString);                        }
+               else if(commandName == "count.seqs")                    {       command = new CountSeqsCommand(optionString);                           }
+               else if(commandName == "count.groups")                  {       command = new CountGroupsCommand(optionString);                         }
+               else if(commandName == "clear.memory")                  {       command = new ClearMemoryCommand(optionString);                         }
                else                                                                                    {       command = new NoCommand(optionString);                                          }
 
                return command;
@@ -486,6 +501,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "classify.seqs")                 {       pipecommand = new ClassifySeqsCommand(optionString);                    }
                else if(commandName == "chimera.ccode")                 {       pipecommand = new ChimeraCcodeCommand(optionString);                    }
                else if(commandName == "chimera.check")                 {       pipecommand = new ChimeraCheckCommand(optionString);                    }
+               else if(commandName == "chimera.uchime")                {       pipecommand = new ChimeraUchimeCommand(optionString);                   }
                else if(commandName == "chimera.slayer")                {       pipecommand = new ChimeraSlayerCommand(optionString);                   }
                else if(commandName == "chimera.pintail")               {       pipecommand = new ChimeraPintailCommand(optionString);                  }
                else if(commandName == "chimera.bellerophon")   {       pipecommand = new ChimeraBellerophonCommand(optionString);              }
@@ -541,6 +557,10 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
                else if(commandName == "set.current")                   {       pipecommand = new SetCurrentCommand(optionString);                              }
                else if(commandName == "make.shared")                   {       pipecommand = new SharedCommand(optionString);                                  }
                else if(commandName == "get.commandinfo")               {       pipecommand = new GetCommandInfoCommand(optionString);                  }
+               else if(commandName == "deunique.tree")                 {       pipecommand = new DeuniqueTreeCommand(optionString);                    }
+               else if(commandName == "count.seqs")                    {       pipecommand = new CountSeqsCommand(optionString);                               }
+               else if(commandName == "count.groups")                  {       pipecommand = new CountGroupsCommand(optionString);                             }
+               else if(commandName == "clear.memory")                  {       pipecommand = new ClearMemoryCommand(optionString);                             }
                else                                                                                    {       pipecommand = new NoCommand(optionString);                                              }
 
                return pipecommand;
@@ -610,6 +630,7 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "chimera.ccode")                 {       shellcommand = new ChimeraCcodeCommand();                       }
                else if(commandName == "chimera.check")                 {       shellcommand = new ChimeraCheckCommand();                       }
                else if(commandName == "chimera.slayer")                {       shellcommand = new ChimeraSlayerCommand();                      }
+               else if(commandName == "chimera.uchime")                {       shellcommand = new ChimeraUchimeCommand();                      }
                else if(commandName == "chimera.pintail")               {       shellcommand = new ChimeraPintailCommand();                     }
                else if(commandName == "chimera.bellerophon")   {       shellcommand = new ChimeraBellerophonCommand();         }
                else if(commandName == "phylotype")                             {       shellcommand = new PhylotypeCommand();                          }
@@ -664,6 +685,10 @@ Command* CommandFactory::getCommand(string commandName){
                else if(commandName == "set.current")                   {       shellcommand = new SetCurrentCommand();                         }
                else if(commandName == "make.shared")                   {       shellcommand = new SharedCommand();                                     }
                else if(commandName == "get.commandinfo")               {       shellcommand = new GetCommandInfoCommand();                     }
+               else if(commandName == "deunique.tree")                 {       shellcommand = new DeuniqueTreeCommand();                       }
+               else if(commandName == "count.seqs")                    {       shellcommand = new CountSeqsCommand();                          }
+               else if(commandName == "count.groups")                  {       shellcommand = new CountGroupsCommand();                        }
+               else if(commandName == "clear.memory")                  {       shellcommand = new ClearMemoryCommand();                        }
                else                                                                                    {       shellcommand = new NoCommand();                                         }
 
                return shellcommand;